Implementing a XDMF/HDF5 Parallel File System in Alya

Alya is a Computational Mechanics (CM) code developed at Barcelona Supercomputing Center, which solves Partial Differential Equations (PDEs) in non-structured meshes, using Finite Element (FE) methods. Being a large scale scientific code, Alya demands substantial I/O processing, which may consume considerable time and can therefore potentially reduce speed-up at petascale. Consequently, I/O task turns out a critical key-point to consider in achieving desirable performance levels. The current Alya I/O model is based on a master-slave approach, which limits scaling and I/O parallelization. However, efficient parallel I/O can be achieved using freely available middleware libraries that provide parallel access to disks. The HDF5 parallel I/O implementation shows a relatively low complexity of use and a wide number of features compared to others implementations, such as MPI-IO and netCDF. Furthermore, HDF5 exposes some interesting aspects such as a shorter development cycle, a hierarchical data format with metadata support and is becoming a de facto standard as well. Moreover, in order to achieve an open-standard format in Alya, the XDMF approach (eXtensible Data Model Format) has been used as metadata container (light data) in cooperation with HDF5 (heavy data). To overcome the I/O barrier at petascale, XDMF & HDF5 have been introduced in Alya and compared to the original master-slave strategy. Both versions are deployed, tested and measured on Curie and Jugene Tier-0 supercomputers. Our preliminary results on the testbed platforms show a clear improvement of the new parallel I/O compared with the original implementation.